A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two- dimensional proton exchange NMR spectroscopy

The formation of S-hydroxymethylglutathione from formaldehyde and glutathione is a central reaction in the consumption of the cytotoxin formaldehyde in some methylotrophic bacteria as well as in many other organisms. We describe here the discovery of an enzyme from Paracoccus denitrificans that accelerates this spontaneous condensation reaction. The rates of S- hydroxymethylglutathione formation and cleavage were determined under equilibrium conditions via two-dimensional proton exchange NMR spectroscopy. The pseudo first order rate constants k(1)* were estimated from the temperature dependence of the reaction and the signal to noise ratio of the uncatalyzed reaction. At 303 K and pH 6.0 k(1)* was found to be 0.02 s(-1) for the spontaneous reaction. A 10-fold increase of the rate constant was observed upon addition of cell extract from P. denitrificans grown in the presence of methanol corresponding to a specific activity of 35 units mg(-1). Extracts of cells grown in the presence of succinate revealed a lower specific activity of 11 units mg(-1). The enzyme catalyzing the conversion of formaldehyde and glutathione was purified and named glutathione-dependent formaldehyde- activating enzyme (Gfa). The gene gfa is located directly upstream of the gene for glutathione-dependent formaldehyde dehydrogenase, which catalyzes the subsequent oxidation of S- hydroxymethylglutathione. Putative proteins with sequence identity to Gfa from P. denitrificans are present also in Rhodobacter sphaeroides, Sinorhizobium meliloti, and Mesorhizobium loti

The rectilinear Steiner tree problem with given topology and length restrictions

We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length restrictions. We want to minimize the total length of the tree. The problem can be formulated as a linear program and therefore it is solvable in polynomial time. In this paper we analyze the structure of feasible embeddings and give a combinatorial polynomial time algorithm for the problem. Our algorithm combines a dynamic programming approach and binary search and relies on the total unimodularity of a matrix appearing in a sub-problem.Comment: 14 page

MOTIVATING ENVIRONMENTAL CITIZEN SCIENTISTS AND OPEN DATA ACQUISITION ON OPENSENSEMAP WITH OPEN BADGES

Citizen science projects making the public part of scientific research are a growing trend and often have a strong geospatial focus with mapping and observation activities on biodiversity or environmental topics. To keep participants engaged, gamification is often used, adding elements of competition and rewards. Digital badges are a common gamification component that can increase participant motivation. Open Badges, an open standard for digital micro-credentials, can be used in citizen science projects to incentivize participants and showcase their achievements. They can also be adapted to open education, where learners can build a portfolio of evidence to demonstrate their achievements and credentials. Open Badges can enhance the learning experience and increase motivation, leading to improved educational outcomes. The use of Open Badges in citizen science and open education aligns with the spirit of collaboration and transparency in science and technology. In this paper we propose a solution linking the openSenseMap, as an open environmental citizen science platform, to myBadges, an Open Badges infrastructure, to allow an automatic issuing of badges for achievements made. A short study reveals first impressions of the proposed solution, its motivational aspects to contribute and improve open data on the platform, and the potential for future work

Complement inhibitor CSMD1 acts as tumor suppressor in human breast cancer

Human CUB and Sushi multiple domains 1 (CSMD1) is a membrane-bound complement inhibitor suggested to act as a putative tumor suppressor gene, since allelic loss of this region encompassing 8p23 including CSMD1 characterizes various malignancies. Here, we assessed the role of CSMD1 as a tumor suppressor gene in the development of breast cancer in vitro and in vivo. We found that human breast tumor tissues expressed CSMD1 at lower levels compared to that in normal mammary tissues. The decreased expression of CSMD1 was linked to a shorter overall survival of breast cancer patients. We also revealed that expression of CSMD1 in human breast cancer cells BT-20 and MDA-MB-231 significantly inhibited their malignant phenotypes, including migration, adhesion and invasion. Conversely, stable silencing of CSMD1 expression in T47D cells enhanced cancer cell migratory, adherent and clonogenic abilities. Moreover, expression of CSMD1 in the highly invasive MDA-MB-231 cells diminished their signaling potential as well as their stem cell-like properties as assessed by measurement of aldehyde dehydrogenase activity. In a xenograft model, expression of CSMD1 blocked the ability of cancer cells to metastasize to secondary sites in vivo, likely via inhibiting local invasion but not the extravasation into distant tissues. Taken together, these findings demonstrate the role of CSMD1 as a tumor suppressor gene in breast cancer

An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude

Low-affinity ligands can be efficiently optimized into high-affinity drug leads by structure based drug design when atomic-resolution structural information on the protein/ligand complexes is available. In this work we show that the use of a few, easily obtainable, experimental restraints improves the accuracy of the docking experiments by two orders of magnitude. The experimental data are measured in nuclear magnetic resonance spectra and consist of protein-mediated NOEs between two competitively binding ligands. The methodology can be widely applied as the data are readily obtained for low-affinity ligands in the presence of non-labelled receptor at low concentration. The experimental inter-ligand NOEs are efficiently used to filter and rank complex model structures that have been pre-selected by docking protocols. This approach dramatically reduces the degeneracy and inaccuracy of the chosen model in docking experiments, is robust with respect to inaccuracy of the structural model used to represent the free receptor and is suitable for high-throughput docking campaigns

Correction: Complement inhibitor CSMD1 acts as tumor suppressor in human breast cancer

This article has been corrected: In Figure 4B, the image of MDA-MB-231 cells expressing CSMD1 is an accidental duplicate of the image showing invaded BT-20 cells expressing CSMD1 in Figure 4A. The correct Figure 4, produced using the original data, is shown below. The authors declare that these corrections do not change the results or conclusions of this paper. Original article: Oncotarget. 2016; 7:76920–76933. https://doi.org/10.18632/oncotarget.1272

The exchange activities of [Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) from methanogenic archaea in comparison with the exchange activities of [FeFe] and [NiFe] hydrogenases

[Fe] hydrogenase (iron–sulfur-cluster-free hydrogenase) catalyzes the reversible reduction of methenyltetrahydromethanopterin (methenyl-H4MPT+) with H2 to methylene-H4MPT, a reaction involved in methanogenesis from H2 and CO2 in many methanogenic archaea. The enzyme harbors an iron-containing cofactor, in which a low-spin iron is complexed by a pyridone, two CO and a cysteine sulfur. [Fe] hydrogenase is thus similar to [NiFe] and [FeFe] hydrogenases, in which a low-spin iron carbonyl complex, albeit in a dinuclear metal center, is also involved in H2 activation. Like the [NiFe] and [FeFe] hydrogenases, [Fe] hydrogenase catalyzes an active exchange of H2 with protons of water; however, this activity is dependent on the presence of the hydride-accepting methenyl-H4MPT+. In its absence the exchange activity is only 0.01% of that in its presence. The residual activity has been attributed to the presence of traces of methenyl-H4MPT+ in the enzyme preparations, but it could also reflect a weak binding of H2 to the iron in the absence of methenyl-H4MPT+. To test this we reinvestigated the exchange activity with [Fe] hydrogenase reconstituted from apoprotein heterologously produced in Escherichia coli and highly purified iron-containing cofactor and found that in the absence of added methenyl-H4MPT+ the exchange activity was below the detection limit of the tritium method employed (0.1 nmol min−1 mg−1). The finding reiterates that for H2 activation by [Fe] hydrogenase the presence of the hydride-accepting methenyl-H4MPT+ is essentially required. This differentiates [Fe] hydrogenase from [FeFe] and [NiFe] hydrogenases, which actively catalyze H2/H2O exchange in the absence of exogenous electron acceptors

Photoinduced electron transfer reactions of phthalimides

The influence of deactivation processes (like hydrogen bonding) on the photodecarboxylation of w-phthalimido potassium carboxylates was studied using a series of N-phthaloyl dipeptides. Furthermore, the decarboxylative addition of unfunctionalized carboxylates and heteroatom-functionalized carboxylates to phthalimides was developed as a highly chemoselective radical addition reaction